Stranger Things Have Occurred
by Waiting for Cas
Summary: Potential threats of S.H.I.E.L.D have been carefully watched for many years. When the time has come to bring in those potentials, anger will be the first instinct, especially if someone gets hurt. S.H.I.E.L.D may have gone over their heads when they realize what those 'potential threats' are capable of.
1. The Beginning of Something Strange

Ok, just some quick things to clear things up.

This is set after Doctor Who: The Day of the Doctor

Also something terrible happened to U.N.I.T and it no longer exists, for the sake of the story.

This is set after the Avengers, Iron Man 3, but most likely before Captain America.

This will have more fandoms than just Doctor Who and the Avengers!

...

The Beginning of Something Strange

To say that Tony Stark was furious would be an understatement. The resent he felt towards S.H.I.E.L.D at the moment was unlike any other. They had abandoned him, leaving him to face killer, exploding, fire monsters on his own, left his girlfriend, Pepper, and the President of the United States for the dead, and they hadn't even bothered to help with the massive clean up efforts. Then, two weeks later, they asked him to go with Agent Barton on a mission in Britain. They hadn't even given him enough time to rebuild Malibu home. He would have rejected the file marked with Top Secret if not for Pepper convincing him otherwise.

The four-hour flight from New York to London would have been fine, except for the fact he stuck on a small jet with two pilots, Clint Barton, and a random Agent that Tony hadn't bothered to remember what came after Agent. Supposedly this "Level 6" Agent was the one that had gathered what little information that was in the file. To be honest, for a potential threat, they had little information. Then again, Tony was pretty sure that S.H.I.E.L.D's motto was eliminate threats before they become threats.

"The thing we are after is not human, so we believe," Agent began.

"Wait," Tony said rising from his seat, "Your saying you don't even know if the person we're after is human?"

"Not exactly," Agent said awkwardly.

"So we could be going after a normal terrorist?" Barton butted in.

"Did you two even read the file?" Agent Whatshisname asked, already knowing the answer.

Both Tony and Clint looked away awkwardly. Nether of them had bothered to. What three pieces of paper rested inside the file covered on their flight over to England.

"Better get reading then," The Agent said through his clenched teeth.

Rolling his eyes, Tony grabbed the device from behind his seat and sat down. He pulled out the memory stick that came with the classified file and placed it on top of the device. Instantly about seventy pictures showed up, and the three pages of documents he hadn't bothered to read. The first thing that stood out to him was that where ever this guy went, so did a blue box. As far as the files went, the guys name was the Doctor, that was it on his name. The strangest part about it was the fact that he seemed to have twelve different faces, each one completely different.

"Almost all these files come from U.N.I.T, what was left of it anyways," Agent answered to the unasked question.

"Wait, you are head Agent on this case and you have found nothing on this guy?" Barton questioned, authority in his voice.

"This man is almost impossible to find. There was nothing on him on any electronic files, which means S.H.I.E.L.D had to recover what we could on him through the paper files at what was left of U.N.I.T. To go through all their paper files took us years. What we could find on him was little. The pictures we gathered were through convenient store security videos. Getting any clean picture of this man is almost impossible, so don't tell me I didn't do any work on this case."

Clint just nodded his head, and continued to read through the files. He was quite interested in why this man always seemed to be with a 50's Police Box. Almost all the pictures with him in it had the blue box near him. Clint actually found this entire file entertaining. Most cases were filled with crazy terrorists, assassins or other murders, but this one was different. It seemed that this Doctor was at several huge historical events, even at the Prince of England's marriage ceremony.

"What's with all the chicks?" was Tony's only question, of course.

"From what we can tell, there the Doctors "company." A girl is often seen with the Doctor, traveling with him. The girl with the blonde hair is Rose Tyler. She has been seen with two of the faces the Doctor has. Her boyfriend Mickey Smith and Rose's mother Jackie Tyler has also been seen associated with the Doctor. The next girl with the black hair is Martha Jones. She studied to be a doctor, but it seems after she left the Doctor, she went and worked for U.N.I.T. Donna Noble is the next women. She's just an average day women. Has a job, is married, nothing too interesting about her. The next two are Amy and Rory Williams. This one is the weirdest case. The two were seen in 2012, then appeared in 1960's, exactly the same. The last known girl to be associated with the Doctor is Clara Oswald. She is the person you two are meeting. We want to find the Doctor, and she's the closest thing we have to find him, so DO NOT MESS UP WHEN YOU TALK TO HER," the Agent shouted at the end.

Both Tony and Clint were silent, contemplating what the Agent had just said.

"Agent Steel, what will we do if she doesn't talk?" Clint asked, knowing the answer.

"We will do what it takes to find the Doctor."

To be honest, Clint hadn't been comfortable with any field missions after the possession of the mind thing. He had killed a lot of Agents and probably innocent people as well. He hadn't quite forgiven himself yet, and neither had more of S.H.I.E.L.D's Agents. He didn't get treated with the same respect as he used to. He had lost most of his friends after his mind being controlled. His only friend that was left was Natasha, she understood. The other "Avengers" had tried to be his friends, but they still didn't trust him fully. The only exception was Thor, he had understood what his brother had done to Clint. actually Thor was great friends with Clint. When Thor came from Asgard, he would often come and visit Barton to see how he was doing. Thor had a huge heart, he just didn't know how to use it all the time.

This was one of the first missions in a while for Clint. He had spent the last few months helping clean up New York and stopping smaller criminals. For Clint, he felt like he was no longer a villain the more he did small things like that.

But to maybe hurt a girl who had done nothing wrong, was taking it to far for Agent Barton.


	2. The Questions are Why?

The Questions are Why?

Steve Rogers missed home. Not the small room he had at S.H.I.E.L.D headquarter, or the apartment he had in modern-day Brooklyn, but the home he had grown up in. He missed the house his mother used to scald him in when he tracked mud inside, the house his dad taught him how to treat a women properly, and the house he learned how to life to the fullest in. He missed the 1940's were people had face to face conversations instead of 'texting' one another, the time were children played outside all day and laughed and laughed. Most of all he missed Peggy. The one women he had fallen truly in love with. Steve missed almost all of it, and he wished constantly that he could go back.

Fury would often send him out on solo missions to distract him. It never worked. It reminded him too much of what happened during World War 2, as they call it now. He wished he would send him on more missions with some of the Avengers. They took his mind off of the past and set in on the present. Captain had really enjoyed what missions he had went on with Natasha. He liked her nothing more than a friend, but her company was always well appreciated.

The hardest part for Steve was going on missions when aliens were involved. It had been hard enough to comprehend cell phones but alien devices that transported people and gods that lived in the stars? It was rough on Steve, trying to wrap his head around it. The bad part for Steve, things were about to get a lot more confusing.

* * *

Steve, Natasha, Bruce and ten other Agents were sitting in a meeting room. they had been called in an hour ago, and they were still sitting there. No one talked or moved. It was dead silent in the room. No one even mad eye contact, they just stared at the front of the room.

"Agents," Nick Fury almost yelled as he walked in, "This is a top priority mission. If you fail this in the slightest way, you will spend the rest of your pathetic lives behind a desk filing paperwork. Do I make myself clear?" A chorus of 'sir yes, sir's' followed after Fury's declaration.

"This may be the most important mission ever done by S.H.I.E.L.D, so we can. Not. Fail," Nick stepped up to the hologram board at the front of the room. Entering a password, the screen filled with photos and other information.

" This is Samuel and Dean Winchester," he explained, clicking on a picture. One of the men was tall with long hair, while the other was shorter and a lot tougher looking, "These two men have committed serious acts of violence, have dug up more than one hundred graves and burned the bones inside, and have done so in a manner of religious symbols. They have also managed to fake their deaths three times. We believe these men are starting some religious cult or hunting some sort of alien crap."

"So your saying that even S.H.I.E.L.D doesn't have much information on what those two boys are doing," Bruce asked quite astonished that two boys have managed to stump a hugely funded operation.

"It isn't just two boys. We have known facts that their father, John Winchester, and a man named Bobby Singer also went around doing the exact same things as them!" the Director flipped through the pictures as he yelled at the group.

"What about the other men, with the black hair?" Natasha asked.

"This is Kevin Tran. A two years ago Kevin just took off one night, from what we could tell, he began to associate with the Winchesters. We don't know why he did it. He was at the top of his class, had a girlfriend and had acceptance top the top collages in America." He flipped to another picture, this one of a man in his mid thirties. "Jimmy Novak. He had a wife, a kid, and a good job. One night, much like Kevin, he just takes off. He is also seen with the Winchesters."

"What do you want us to do?" Captain Rogers questioned.

"I want all four of them back here alive-," Fury began.

"What about the other two?" interrupted Bruce.

"John Winchester and Bobby Singer are both dead," snapped the Director, "The other four were last seen in Lebanon, Kansas. Find them, bring them back to S.H.I.E.L.D...ALIVE! DO I MAKE MYSELF CLEAR."

"Sir yes sir," echoed back at Fury.

"You leave in 0500 hours tomorrow, Captain Rogers will be commander, be ready and DO NOT KILL THEM," was Fury's final words before leaving

* * *

"We waited there for an hour and he talked for less than fifteen minutes," Bruce commented, looking at Steve and Natasha who were sitting across from him.

"I hadn't even heard of these guys till now, and I've heard of everyone," was Natasha's only remark.

The three of them sat in silence at the cafeteria table, thinking about what Fury had said.

"I understand why the boy ran away, pressure and all, but why Jimmy," Bruce commented off handedly, "He had a wife and a daughter, why do you think he left?"

"Money, debt, didn't love them any more, had an affair, there's a thousand reasons Bruce," Romanoff explained, not really paying attention.

None of them were really paying attention to each other. Steve was trying to figure out a plan so that no one would end up getting injured, Natasha had her mind set on why she had been called to play apart in this mission, and Bruce was trying to figure out three things. Why did Jimmy leave his family? Why did Fury give them so little information? Why did the four boys need to be kept alive?


	3. Gone

Gone

Clara Oswald loved her job as a teacher. Her seventh year students were well-behaved, the other staff members were great, and her hours were perfect! Of course there were the downs of being a teacher. The marking of assignments, the long hours of planning, and of course the bratty kids that never stopped talking. Happily, the pro's outweighed the cons so teaching was great. Well, that was until the two men showed up.

The week had flown by for Ms. Oswald. It always seemed that there was never enough time in the week for her to get everything done. Often during the week she would have to stay after school and finish up marking, and/or planning. It seemed to be an endless cycle lately. Go to school, teach school, stay after school, go home, go to school...Then again, almost all the other teachers seemed to caught in the endless trap as well. The only thing that got her out of the loop was the Doctor. Every once in a while he would swoop down in his not so little blue box and bring her on an adventure. Sadly for her, the one day that she needed the Doctor, was the day he never came.

* * *

It had been Clara's third time that week that she had stayed late after school. By this point she had been marking for an hour and her not so comfy chair was becoming even less comfortable by the minute. All she wanted to do was go home to at least finish marking, but she knew she would lose some ones assignment and she would not be able to find it until summer. Clara had been so distracted by her thoughts, she had missed the knocks on her classroom door.

When the knocks came again, it had confused Clara. Teachers would just walk in, students would knock then poke their heads in, and anyone else would have been called in ahead by the office, so who were these people?

Confused, Clara called to the person(s) outside "Um, come in?"

Two men walked in. Both men were dressed in a bit fancier clothing and walking with authority in their steps. One had dark brown, almost back hair with a clean-shaven beard that looked extremely familiar. The other man had short, light brown hair and was just slightly taller than the other man.

"Can I help you?" Clara asked the two men.

"Yes actually you can," the man with the light brown hair answered, "You are Clara Oswald, right," Clara nodded her head confused, "Ok that's good. We are looking for a man named the Doctor..."

As soon as he said that, red flags went off in her head. Very few knew about the Doctor, and of the few that did, almost all of them wanted to harm him in some way. She slowly reached for her desk drawer. Inside, at the bottom of the top drawer, there was the Stunner. It would stun any life form, except humans, and put a tracking device in the life form, no matter what life form. It was a safety feature so no-one could use it against her. The Doctor had given this to her after the kidnapping incident in Norway, the planet. It had taken the Doctor three days to find her, that's why he had given her the Stunner.

"Doctor?" Clara chose her words carefully, "Doctor who?" She grabbed her Stunner out of her drawer and spun her chair around to face the other way so they didn't notice. Through the reflection of the computer screen she watched them.

"We know that you know who the Doctor is, so don't get smart with us," light brown hair said, anger already evident.

"Ok, ok," Clara replied, just turning her head to face them, "There is Doctor Mary, my regular doctor, there's Doctor Cameron, my optometrist, there is..."

"The. Doctor," light brown hair snapped and surged towards her.

Panicking, Clara jumped out of her chair, holding the Stunner out in front of her. The man instantly stopped moving towards her, and both men put their hands in the air.

"There is no need to panic," the other man spoke for the first time, "I'm Tony and that Clint. We just want to talk, ok?" His voice towards the end changed, as if he was suggesting something. Of course Clara had her eyes fixed on only Tony when he was talking, so she hadn't seen the other man, Clint, come up behind her.

Clara had shot as soon as she had felt something cold touch her neck. Unluckily for Tony, he was where her stunner had been pointed.

The last thing she remembered before blacking out was that Tony did not fall over. These men were humans.

* * *

"She could have killed me," Tony complained as they wheeled Clara out on her desk chair.

"That was the point," Clint smirked at him.

Clint was actually a very sarcastic, good-natured guy, if you got to know him. Otherwise he would seem like the kind of guy that plans how he's going to kill you the moment you meet him. Actually, he did that either way.

"Well aren't you a bucket of sunshine today," was all Tony could mumble back. He was actually quite mad at Clint. Firstly, he had taken one of his newest projects and used it without his permission. It was a small metal device that when placed on your skin sends electric shocks to the part of your that makes you sleep. He hadn't tested it yet, so it could have killed the girl as well. The second thing he was mad about was that he had almost gotten him killed. If that gun hadn't been loaded, or hadn't worked, he could have been dead now.

"Are you sure she is still alive, I mean, she's not moving,"

"No, she's totally dead," Clint rolled his eyes.

Tony rolled his eyes right back, and changed the subject, "I still can't believe she didn't notice when we set her clock back two hours. Like really, there is no one within an hour of the school this late, how did she not notice that there was no-one here? Or the helicopter landing like three yards from the school?"

"Did you not do any reading?" Tony shook his head no, "Of course not. This is one of the most private schools in England. Its sound proof, bullet proof, and ever single person and everyone in their family has a security check done on them. It's like a prison." There was a moment's pause, " How are we going to get her down the stairs?"

* * *

The Doctor had been waiting. Five hours to be exact. He had come on a Saturday morning, nine am sharp. Clara should have looked out her window by now and noticed the blue box, but she hadn't. He tried to think positively, she was only at a friend's house, or out for a walk, or at the school. Even though his thoughts were positive, he knew in his heart something was wrong.

Getting up from the floor, the Doctor closed his book and went to the door. He didn't want to go outside. He didn't want to find Clara hurt, or worse. Taking a deep breath, he stepped outside. It was a bright sunny day without a cloud in the sky. Why was it always like that? The worst of times always seemed like the nicest. As he walked towards Clara's apartment, he searched the field desperately for her, but she was not to be found. The Doctor climbed three flights of stairs to Clara's small apartment. He knocked on her door, hoping desperately that she would open her door, but she didn't. He tried three more times with no reply.

Instead of trying Clara's door again, he tried the neighbor's door. Inside there was a younger women with three kids. Jacqueline was her name. She had often bumped into the Doctor and Clara and was convinced that the two of them were a couple.

When Jacqueline opened her door, her bright smile turned into a sad frown. She quickly stepped forward and gave the Doctor a hug and whispered in his ear, "I'm so sorry, I'm so so sorry."

The Doctor pried Jacqueline's hands of off him, his fears coming more true by the second, "What's wrong, why are you sorry?" he asked, but already knew the answer.

"You didn't hear?" the Doctor shook his head, "I'm so sorry, but Clara went missing two days ago."


	4. I Told You

Let's just say for the sake of the story, Slumber Party, never happened. For Sam and Dean, this is sometime just before Holy Terror, for Cas, it is sometime during the time of Holy Terror. Also, I'm sorry I took so long to update...

* * *

"...No it wasn't, I would know. I've been hunting for years and not once have I come across even one. . . It was probably some sort of trickster making everyone believe that it was aliens but it was reality it was probably demons or something. . .No! I did not say that!. . .For the last time, the Attack of 'aliens' in New York was by actual aliens. . . No I have not seen the bodies they cleared them out to fast. . .How about I prove it to you in person. . .Yes meet us in Lebanon in that little restaurant on Second Street. . . Two hours? Where are you? Hello? Hello? Damn it!" Dean yelled into his phone.

"Who was that?" Sam asked walking into the Library.

"Charlie. She is convince that the attack on New York was because of aliens. Aliens! She is coming town to prove me wrong, that's the only reason. Unbelievable."

"Is she coming to here," Sam questioned, referring to the Bunker.

"No, we're meeting her Lebanon in a couple of hours," Dean sighed, slouching in his chair.

"Ok," Sam paused, "Should we bring Kevin, he hasn't seen society in a while, or even felt fresh air in at least a month."

"I'm down with that, if you can get Kevin ready," Dean stated, before getting up.

"Aren't you going to help?"

"Nope. Have fun getting Kevin ready, I'm getting some books on aliens."

* * *

After about ten minutes of trying to convince Kevin, Sam finally got him to agree to come into town. The next issue though was whether or not to bring the tablet.

"It would be safer with me Sam," Kevin had said stubbornly for tenth time.

"But what if the angels got a hold of you, or a gang of demons, or something even worse. Then they'd have the tablet and the translator, and then they could uncover things that could put anyone in danger."

"But-"

"Plus no demon, angels, or even humans can get in here without a key so its safe in here," Sam pointed out.

Kevin paused for a moment, "Fine, but can I at least hide it?"

Sighing with relief that the argument was finally over, Sam nodded his head. Looking a little more comfortable with the situation, Kevin grabbed the tablet and left the his bedroom.

Kevin had to admit to himself, he was being over-cautious. Ever since Crowley had murdered his mother, he had been over the top on making sure everything was secure. The Winchesters didn't know it, be he checked every door in the building at night and had drawn thousands of symbols on every wall just to be sure that nothing could get in.

Then there was a plan B) if anything did get in. It was all about protecting the tablet. If he died, there was always another prophet, if the Winchester's died, there was always more hunters. If the tablet was in the wrong hands, every angel could be killed. He would not let that happen. Over the past few months he had adopted one of the store rooms for his project. He had taken out every tile on the floor and had drawn warding symbols on the bottom of everyone. It had taken him ages, but it would be worth it in the end. The next thing he had created was a box to go underneath one of the tiles. It was also covered in symbols. The last thing that he had done in case of having to leave the tablet was literally covering the room in holy water.

Even after he had the tablet in place, he had a worrying feeling that something was going to go wrong.

* * *

"Hey bitches," Charlie called over the loud noises of the diner She stepped forward and gave both Dean and Sam a hug.

"Hey Charlie," Sam smiled at her, "Kevin this is Charlie. Charlie, this is Kevin," he pointed at Kevin.

"Hi Kevin, Charlie smiled at him, sitting down at her booth and gesturing the boys to sit down wither her.

"Why the hell do you think aliens of all things attacked New York? Really, of all the things that you could have thought of, why aliens?" Dean asked, while Sam rolled his eyes.

"Well mister know-it-all, if you haven't noticed, none of the details match up with any lore of any culture, at all," pulling out her iPad, Charlie scrolled through her list of monsters, "It can't have been any sort of tricking god, there were to many people to, what would you call it, 'hypnotize.' It couldn't have been a ghost, ghoul, dragon, demon, leviathan, or any sort of monster that you have hunted, so it's obviously an alien. Plus it came through a giant portal from space. Beat that."

"Look Charlie, I've been hunting forever, basically, and not once have I come across an alien, or and I doubt any other hunter has either," Dean started to explain, "The last time we encountered 'aliens,' it ended up just being fairies, and the time before that was an angel disguised as a fake god. See what I mean, there is no such thing as aliens!"

"That's the best you got?" Charlie asked mockingly.

"Oh, were just starting," Dean smiled at her in a 'we're just getting started' way.

* * *

Eight cups of coffee and three books from the bunker on aliens later, the two had still not agree. Sam and Kevin had gotten bored a while back, but Dean had forced them to stay for 'moral support.'

"Sam what do you think?" Charlie asked him, hoping that he would be on her side.

"Sorry Charlie, but I agree with Dean. Just because a good population of the world believes in them, that doesn't mean that it's true. Sorry" Sam apologize when Charlie gave him a death glare.

"What about you Kevin? Don't you agree with me?" Charlie asked, desperation in her voice.

Kevin thought about it for a second, "Well, just a few years ago I didn't even think anything stranger than killer wasps existed, now demons, leviathan, and angels exist, so why can't aliens exist too."

"Really Kevin, aliens?" Sam said at the same time as Dean had given the death glare to Kevin.

"Aliens? Aliens? You believe in aliens?"

Thus that began a new argument that lasted another hour until a waitress came up to them saying that the restaurant was closing soon. All of them tossed what change they had in their pockets on the table and left the restaurant, still not in agreement.

"Can we argue about this later," Kevin sighed, "I'm ready to get back to the Bunker and go to bed."

"Ya, that sounds good," Sam agreed yawning, "We can all take the Impala back and we can pick up your car tomorrow Charlie."

All in agreement, the four of them piled in the Impala. The drive back to the Bunker was quite except for the faint sound of ACDC. By now it was dark, and the stars were beginning to appear. All was peaceful, until the sound of a helicopter was heard. It had started off as a soft buzzing noise, but gradually got louder. Sam was the first to notice.

"What is that noise?" Sam asked, turning the volume down all the way and straining to hear it. For a moment, no one heard anything, then a sound like a buzzing fly became clear.

"Son of a bitch!" Dean yelled. He quickly turned off the headlights and stopped the car. All of them prayed that the helicopter missed them, but their luck was at a loss. A bright white light came in through the windows, lighting up the entire car.

Instantly, Dean slammed his foot on the gas, trying to lose the helicopter. He swerved in and out of the ditch and all over the road, but it was no use. The light wasn't going anywhere.

"Who are they?"

"How did they find us?"

"Everyone stay cool!"

"Are they angels, demons, what are they!"

The four voices muddled together, all of them panicky.

"DEAN WATCH OUT!" Sam yelled.

The light that was on them was now pointing directly in front of them. It was some sort of military set up. There were three large military S.U.V.'s and about twenty people pointing guns at their car.

Dean slammed on his brakes and stopped a good twenty feet before the people in front of them.

"What the hel!" Dean yelled.

"Reverse! Reverse!" Sam cried.

Dean pulled the throttle ready to reverse, when more people with guns came out behind them. They were surrounded on all sides. The helicopter was floating above them, keeping the light on them.

"Guys," Charlie whispered, "What are we going to do?"

Dean slowly moved his hand forward and turned off the ignition.

"We are going to stay calm and wait," Dean replied.

After a few second, a man came out from behind the others. He was wearing a blue and red suit and had some sort of shield attached to his arm. Dean would have made a comment on it (and not a good one) but there were three other people in the car, and he did not want to put their lives in danger. The man in the suit stepped closer to the Impala, and raised a megaphone to his mouth.

"Please step out of the vehicle with your hands raised in the air,' he started, "We do not wish for any of you to be harmed." He lowered the megaphone, waiting for them to comply.

"What do we do?" Kevin began to panic, "They always say we don't want to hurt you, but they always do! Dean what about the tablet, if we die, the angels have no chance getting back to heaven at all, even if Crowley says that there wasn't a chance anyways!"

"Calm down Kevin. Everything will be just fine. We are going to step out slowly and hope we don't get killed, ok?" Sam explained. everyone slowly nodded their heads, hoping this time their luck wouldn't run out.

"Are you sure that we are going to be fine Sam?" were the last words, spoken by Charlie, before they got out.

With their hands raised, they exited the Impala. Kevin was shaking with fear, Charlie had put on a brave front, trying not to show fear, and the Winchesters came out with their normal attitude towards things. Show no fear, and get ready to fight.

"Thank-you," the blue and red man said through the megaphone, "We appreciate your co-operation," he paused for a moment, "We are also very sorry we had to do this, it is for safety measures."

Before anyone had a chance to move, four shots fire, all of them hitting their targets. The four of them collapsed to the ground, and the last thing Sam saw was Kevin's face saying 'I told you something bad was going to happen.'


End file.
